Pipeline scheduling with input port constraints for an FPGA-based biochemical simulator

Tomoya Ishimori; Hideki Yamada; Yuichiro Shibata; Yasunori Osana; Masato Yoshimi; Yuri Nishikawa; Hideharu Amano; Akira Funahashi; Noriko Hiroi; Kiyoshi Oguri

doi:10.1007/978-3-642-00641-8_43

Pipeline scheduling with input port constraints for an FPGA-based biochemical simulator

Tomoya Ishimori, Hideki Yamada, Yuichiro Shibata, Yasunori Osana, Masato Yoshimi, Yuri Nishikawa, Hideharu Amano, Akira Funahashi, Noriko Hiroi, Kiyoshi Oguri

Research output: Contribution to journal › Conference article › peer-review

3 Citations (Scopus)

Abstract

This paper discusses design methodology of high-throughput arithmetic pipeline modules for an FPGA-based biochemical simulator. Since limitation of data-input bandwidth caused by port constraints often has a negative impact on pipeline scheduling results, we propose a priority assignment method of input data which enables efficient arithmetic pipeline scheduling under given input port constraints. Evaluation results with frequently used rate-law functions in biochemical models revealed that the proposed method achieved shorter latency compared to ASAP and ALAP scheduling with random input orders, reducing hardware costs by 17.57 % and by 27.43 % on average, respectively.

Original language	English
Pages (from-to)	368-373
Number of pages	6
Journal	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume	5453
DOIs	https://doi.org/10.1007/978-3-642-00641-8_43
Publication status	Published - 2009
Event	5th International Workshop of Applied Reconfigurable Computing, ARC 2009 - Karlsruhe, United States Duration: 2009 Mar 16 → 2009 Mar 18

ASJC Scopus subject areas

Theoretical Computer Science
Computer Science(all)

Access to Document

10.1007/978-3-642-00641-8_43

Cite this

Ishimori, T., Yamada, H., Shibata, Y., Osana, Y., Yoshimi, M., Nishikawa, Y., Amano, H., Funahashi, A., Hiroi, N., & Oguri, K. (2009). Pipeline scheduling with input port constraints for an FPGA-based biochemical simulator. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 5453, 368-373. https://doi.org/10.1007/978-3-642-00641-8_43

Pipeline scheduling with input port constraints for an FPGA-based biochemical simulator. / Ishimori, Tomoya; Yamada, Hideki; Shibata, Yuichiro et al.

In: Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Vol. 5453, 2009, p. 368-373.

Research output: Contribution to journal › Conference article › peer-review

Ishimori, T, Yamada, H, Shibata, Y, Osana, Y, Yoshimi, M, Nishikawa, Y, Amano, H , Funahashi, A, Hiroi, N & Oguri, K 2009, 'Pipeline scheduling with input port constraints for an FPGA-based biochemical simulator', Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), vol. 5453, pp. 368-373. https://doi.org/10.1007/978-3-642-00641-8_43

@article{42acbe497d39463d8de07e813e4847cf,

title = "Pipeline scheduling with input port constraints for an FPGA-based biochemical simulator",

abstract = "This paper discusses design methodology of high-throughput arithmetic pipeline modules for an FPGA-based biochemical simulator. Since limitation of data-input bandwidth caused by port constraints often has a negative impact on pipeline scheduling results, we propose a priority assignment method of input data which enables efficient arithmetic pipeline scheduling under given input port constraints. Evaluation results with frequently used rate-law functions in biochemical models revealed that the proposed method achieved shorter latency compared to ASAP and ALAP scheduling with random input orders, reducing hardware costs by 17.57 % and by 27.43 % on average, respectively.",

author = "Tomoya Ishimori and Hideki Yamada and Yuichiro Shibata and Yasunori Osana and Masato Yoshimi and Yuri Nishikawa and Hideharu Amano and Akira Funahashi and Noriko Hiroi and Kiyoshi Oguri",

year = "2009",

doi = "10.1007/978-3-642-00641-8_43",

language = "English",

volume = "5453",

pages = "368--373",

journal = "Lecture Notes in Computer Science",

issn = "0302-9743",

publisher = "Springer Verlag",

note = "5th International Workshop of Applied Reconfigurable Computing, ARC 2009 ; Conference date: 16-03-2009 Through 18-03-2009",

}

TY - JOUR

T1 - Pipeline scheduling with input port constraints for an FPGA-based biochemical simulator

AU - Ishimori, Tomoya

AU - Yamada, Hideki

AU - Shibata, Yuichiro

AU - Osana, Yasunori

AU - Yoshimi, Masato

AU - Nishikawa, Yuri

AU - Amano, Hideharu

AU - Funahashi, Akira

AU - Hiroi, Noriko

AU - Oguri, Kiyoshi

PY - 2009

Y1 - 2009

N2 - This paper discusses design methodology of high-throughput arithmetic pipeline modules for an FPGA-based biochemical simulator. Since limitation of data-input bandwidth caused by port constraints often has a negative impact on pipeline scheduling results, we propose a priority assignment method of input data which enables efficient arithmetic pipeline scheduling under given input port constraints. Evaluation results with frequently used rate-law functions in biochemical models revealed that the proposed method achieved shorter latency compared to ASAP and ALAP scheduling with random input orders, reducing hardware costs by 17.57 % and by 27.43 % on average, respectively.

AB - This paper discusses design methodology of high-throughput arithmetic pipeline modules for an FPGA-based biochemical simulator. Since limitation of data-input bandwidth caused by port constraints often has a negative impact on pipeline scheduling results, we propose a priority assignment method of input data which enables efficient arithmetic pipeline scheduling under given input port constraints. Evaluation results with frequently used rate-law functions in biochemical models revealed that the proposed method achieved shorter latency compared to ASAP and ALAP scheduling with random input orders, reducing hardware costs by 17.57 % and by 27.43 % on average, respectively.

UR - http://www.scopus.com/inward/record.url?scp=67249119982&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=67249119982&partnerID=8YFLogxK

U2 - 10.1007/978-3-642-00641-8_43

DO - 10.1007/978-3-642-00641-8_43

M3 - Conference article

AN - SCOPUS:67249119982

SN - 0302-9743

VL - 5453

SP - 368

EP - 373

JO - Lecture Notes in Computer Science

JF - Lecture Notes in Computer Science

T2 - 5th International Workshop of Applied Reconfigurable Computing, ARC 2009

Y2 - 16 March 2009 through 18 March 2009

ER -

Pipeline scheduling with input port constraints for an FPGA-based biochemical simulator

Abstract

ASJC Scopus subject areas

Access to Document

Other files and links

Fingerprint

Cite this